I actually experience a similar phenomena. People do not like to sit next to me if they can avoid it. But I assume this is for a different reason. I'm fat.
I am not insulted by this. To the contrary, it makes perfect sense. If you are going to sit next to someone, you want as much space as possible. As between me and the skinny guy on the other side of the aisle, where would you go first?
This leads me to wonder if there is any good research on this subject. Certainly there are things people do to discourage others sitting next to them. But leaving these aside, do we see clearly defined tendencies to sit next to certain people as trains fill? And do these vary by modes of transportation?
My initial theory would be that a variety of factors go into it for everyone (assuming you actually are looking for a seat -- let's exclude those who stand by choice). Some are more obvious (body odor, condition of open seat), some less obvious (thin over fat) and some even less obvious (people like me v. not like me). It may also have to do with position in the car (i.e., how far do you walk before giving up hope of a totally open seat?).